Structure of PDB 8cd1 Chain N Binding Site BS01

Receptor Information

>8cd1 Chain N (length=118) Species: 208964 (Pseudomonas aeruginosa PAO1)

MRHRKSGRHLSRTSAHRKAMFQNMAVSLFEHELIKTTLPKAKELRRVAEP
LITLAKEDSVANRRLAFDRTRSKAAVGKLFNDLGKRYANRPGGYLRILKC
GFRAGDNAPMAYVELVDR

Ligand information

>8cd1 Chain A (length=2883)

gucaagugaagaagcgcauacgguggaugccuuggcagucagaggcgaug
aaagacgugguagccugcgaaaagcuucggggagucggcaaacagacuuu
gauccggagaucucugaaugggggaacccaccuaggauaaccuagguauc
uuguacugaauccauaggugcaagaggcgaaccaggggaacugaaacauc
uaaguacccugaggaaaagaaaucaaccgagauucccuuaguaguggcga
gcgaacggggauuagcccuuaagcuucauugauuuuagcggaacgcucug
gaaagugcggccauagugggugauagccccguacgcgaaaggaucuuuga
agugaaaucaaguaggacggagcacgagaaacuuugucugaacauggggg
gaccauccuccaaggcuaaauacuacugacugaccgauagugaaccagua
ccgugagggaaaggcgaaaagaaccccggagaggggagugaaauagaacc
ugaaaccguaugcguacaagcagugggagccuacuuguuaggugacugcg
uaccuuuuguauaaugggucagcgacuuauauucaguggcaagcuuaacc
guauaggguaggcguagcgaaagcgagucuuaauagggcguagucgcugg
guauagacccgaaaccgggcgaucuauccaugagcagguugaagguuagg
uaacacugacuggaggaccgaacccacucccguugaaaagguaggggaug
acuuguggaucggagugaaaggcuaaucaagcucggagauagcugguucu
ccucgaaagcuauuuagguagcgccucauguaucacucugggggguagag
cacuguuucggcuagggggucaucccgacuuaccaaaccgaugcaaacuc
cgaauacccagaagugccgagcaugggagacacacggcgggugcuaacgu
ccgucgugaaaagggaaacaacccagaccgccagcuaaggucccaaaguu
gugguuaagugguaaacgaugugggaaggcuuagacagcuaggagguugg
cuuagaagcagccacccuuuaaagaaagcguaauagcucacuagucgagu
cggccugcgcggaagauguaacggggcucaaaccacacaccgaagcugcg
ggugucacguaagugacgcgguagaggagcguucuguaagccugugaagg
ugaguugagaagcuugcuggagguaucagaagugcgaaugcugacaugag
uaacgacaaugggugugaaaaacacccacgccgaaagaccaaggguuccu
gcgcaacguuaaucgacgcaggguuagucgguuccuaaggcgaggcugaa
aagcguagucgaugggaaacagguuaauauuccuguacuucugguuacug
cgauggagggacggagaaggcuaggccagcuuggcguugguuguccaagu
uuaaggugguaggcugaaaucuuagguaaauccgggguuucaaggccgag
agcugaugacgagucgucuagaugacgaagugguugaugccaugcuucca
agaaaagcuucuaagcuucagguaaccaggaaccguaccccaaaccgaca
cagguggucggguagagaauaccaaggcgcuugagagaacucgggugaag
gaacuaggcaaaauggcaccguaacuucgggagaaggugcgccggcuagg
gugaaggauuuacuccguaagcucuggcuggucgaagauaccaggccgcu
gcgacuguuuauuaaaaacacagcacucugcaaacacgaaaguggacgua
uagggugugacgccugcccggugccggaagguuaauugaugggguuagcg
caagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaa
cgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacga
auggcguaacgauggcggcgcugucuccacccgagacucagugaaauuga
aaucgcugugaagaugcaguguauccgcggcuagacggaaagaccccgug
aaccuuuacuguagcuuugcacuggacuuugagccugcuuguguaggaua
ggugggaggcuuugaagcguggacgccaguucgcguggagccauccuuga
aauaccacccuggcaugcuugagguucuaacucugguccguaauccggau
cgaggacaguguauggugggcaguuugacuggggcggucuccuccuaaag
aguaacggaggaguacgaaggugcgcucagaccggucggaaaucggucgc
agaguauaaaggcaaaagcgcgcuugacugcgagacagacacgucgagca
gguacgaaaguaggucuuagugauccggugguucuguauggaagggccau
cgcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaa
gaguucauaucgacggcgguguuuggcaccucgaugucggcucaucacau
ccuggggcugaagccggucccaaggguauggcuguucgccauuuaaagug
guacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugc
cguggacguuugagauuugagaggggcugcuccuaguacgagaggaccgg
aguggacgaaccucugguguuccgguugucacgccaguggcauugccggg
uagcuauguucggaaaagauaaccgcugaaagcaucuaagcgggaaacuu
gccucaagaugagaucucacugggaacuugauuccccugaagggccgucg
aagacuacgacguugauaggcuggguguguaagcguugugaggcguugag
cuaaccaguacuaauggcccgugaggcuugacc

<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<....
..<<<<<<....(((.>>>.....<<<<<<.<.<<<))).....>>>...
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>
......>>>>>.>.........<<....>>...<<<<<.....<<.....
>>....>>>>>...(((.....<<<<<<..<<<<<<.<<<...<<<.<..
....>.>>>((......<<<.....))>>>...>>>...>>>>>>..>>>
>>>...........<<<<<<<<.........>>>>>>>>......<<<<<
..<<<<>>>>>..)))......]].>>>>>>>.]]...............
<<....>>....]].........<<<<.....>>>>..............
....>>>>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>.
..<.<........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<
.....>>...>>>...<<....>>..<<<<.....>>>>...>>>>>>>>
>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<<...<<<<<<.
.....>>>>>>...>.>>>...<<<.<<.<<........>>.>>>>>...
.>>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<
<<<<....<<<<<....>>>>>.<<<<<<<<..<<<<<<<<<.....<<<
...<<<.<<<<...<<.<<<.......>>>..>>...>>>>.>>>..>>.
>.....>>>>>.>>>>....>>>>>>>.>...<<<<<<<<<<......>>
>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<
<<<<<...........<<..<<<<<..<<........<<<<<.<<...<<
<.........>>>...>>........<<<......>>>..>>>>>....>
>..>>>>>.>>...........)))......>>>>>>.>>>...>>>>>>
><<<<<<......>>>>>>....>>>>>>..<<<<<...<<<......<<
<<<<<<....>>>>>>>>...>>>..>>>>>........>>>>>><....
..<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<<<<<...<<<...<<<...
.>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<
<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>>
<<..<<<....<<<.<<<<<<<..<<.....>>.>>>>>>>...>>>...
.>>>...>><..<<<<<<..>>>>>>...>>>>>>...>>>...>>>.>.
.......>>>>...>>....>>>>>>>>>>>>>>>..>>.....<<....
..>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<
...............<<<<<....<<..>>.....>>>>><<<<<<<<<<
<<...<<<.....>>>....>>>>>>>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<<.......<<<<<<.<<.
...>>..>>>>>>.......>>>>>>>>>..>>>>><<<...........
..>>>........<...........<<<<<<.....>>>>>>.....>..
..>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>..
...<<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[
[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<.<............
<<<<....<...........<<........>>........>.........
.....>>>>...>.>.>>>>>>>>>>>...<<<.<<<<<<.....>>>>>
>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.....
......>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>..
...<<.[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>
>.<<<....>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>
>>.............>>>>..]]>>>>.......<<<<...<<<<<<...
<<.......>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..
<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>
>>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]..)))>>
>>>>>>....<<<<<<<...<<<<..<<<<<<<...............>>
>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>..>>>>>.
..>>>>.>>>>>...<<<....<<<<<...........>>>>>....>>>
.>>>>.......>>>>>>>..<<<<<.....>>>>>.....<<<<<<<<<
.......>>>>>....<<<<<<<<..<<.....<<<<....>>>>....>
>...>>>>>.>>>...>>>>.....>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cd1 70S-PHIKZ014 PHIKZ phage protein occupied ribosome
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): M1 R2 H3 R4 K5 S6 R8 H9 L10 S11 R12 S14 H16 R17 K18 M20 N23 S27 H31 I34 T36 T37 P39 K40 K42 R45 T53 R63 R64 D68 R71 K73 R90 P91 G92 G93 R96 K99 R103 D106 N107 A108
• Binding residue (residue number reindexed from 1): M1 R2 H3 R4 K5 S6 R8 H9 L10 S11 R12 S14 H16 R17 K18 M20 N23 S27 H31 I34 T36 T37 P39 K40 K42 R45 T53 R63 R64 D68 R71 K73 R90 P91 G92 G93 R96 K99 R103 D106 N107 A108

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cd1, PDBe:8cd1, PDBj:8cd1
• PDBsum: 8cd1
• PubMed: 38443577
• UniProt: O52761|RL17_PSEAE Large ribosomal subunit protein bL17 (Gene Name=rplQ)